From: Primmer et al. 2013 Annotated genes and non-annotated genomes: crossspecies use of Gene Ontology in ecology and evolution research
Supplementary Appendix S2- Enrichment test differences when using ALL vs.
non-IEA evidence codes: Case study from a previously published dataset
(Papakostas et al., 2010).
Papakostas et al. (2010) used mass spectrometry to describe the proteomic profile of
two early life stages, namely eyed-egg and hatching stage, of European grayling
(Thymallus thymallus). They identified 213 proteins in the eyed-egg stage and 239 in
the hatching stage and, among others, performed functional enrichment analyses using
gene ontologies. They used the Danio rerio genome as a gene reference set for the
overrepresentation tests, and hypergeometric analysis was set at the 0.05 level of
significance after Benjamini-Hochberg FDR multiple-testing correction.
Here we used the same gene lists and enrichment settings to investigate differences in
the results when using all evidence codes or when omitted the IEA evidence from
gene annotation. We used the ClueGO (Bindea et al., 2009) Cytoscape (Shannon et
al., 2003) plugin to describe the functional properties of the gene lists in each case by
identifying clusters of functionally related GO terms. To assess the functional
similarity of the generated lists of significant GO terms we also calculated their
semantic similarity using G-Sesame (Du et al., 2009). Annotations were as of 10 JUL
2012. Currently there are more than 139000 annotations assigned to Danio rerio
genes out of which about 22% are non-IEA.
In Fig. 1 we show the numbers of different and shared overrepresented GO terms in
each case. In Suppl. Table 3 we report the five most significant GO terms for
biological process, molecular function, and cellular component. Suppl. Table 4 has all
the enriched GO terms in each case. Semantic similarity was found 0.714 between
ALL vs. not-IEA for eyed-egg stage and 0.727 for hatch stage.
Although many terms were found significant either in ALL or in non-IEA cases
(Fig.1), very similar of even the same GO terms were in the list of five most
significant ontologies (Suppl. Table 3). Also, the semantic similarity of the enriched
GO terms was indicative of their high functional relatedness as values >0.7 are
considered as high similarity (Du et al., 2009).
Reference cited
Bindea G, Mlecnik B, Hackl H, et al. (2009) ClueGO: a Cytoscape plug-in to decipher
functionally grouped gene ontology and pathway annotation networks.
Bioinformatics, 25, 1091–1093.
Du et al. (2009) gene similarity analysis and knowledge discover. Nucleic Acids
Research, 37: W345-W349.
Papakostas S, Vollestad LA, Primmer CR, Leder EH (2010) Proteomic profiling of early
life stages of European grayling (Thymallus thymallus) Journal of Proteome Research
9, 4790-4800
Shannon P, Markiel A, Ozier O, et al. (2003) Cytoscape: a software environment for
integrated models of biomolecular interaction networks. Genome Research 13:2498504
Fig. 1. The number of shared significant GO terms with and without IEA evidence
codes in the gene lists of the eyed-egg and hatching stages.
EYED-egg significant GO terms
99
42
ALL evidence codes
13
not IEA
HATCH significant GO terms
104
ALL evidence codes
54
18
not IEA
Suppl. Table 3: The five most significant GO terms for biological process, cellular
component, and molecular function in the eyed-egg and hatching stage gene lists. In
bold are terms in common in the top5 list in ALL vs. not-IEA analysis.
EYED-EGG ALL
EYED-EGG not-IEA
Biological Process
Translation
Ribosomal small subunit biogenesis
Translational elongation
Cellular component biogenesis at cellular level
Ribonucleoprotein complex biogenesis
Ribosomal small subunit biogenesis
Ribonucleoprotein complex biogenesis
Cellular component biogenesis at cellular level
Translation
Ribosome biogenesis
Cellular Component
Ribosome
Ribonucleoprotein complex
Cytoplasm
Intracellular non-membrane-bounded organelle
Cytoplasmic part
Ribosome
Small ribosomal subunit
Ribosomal subunit
Cytosolic ribosome
Cytosolic small ribosomal subunit
Molecular Function
RNA binding
Unfolded protein binding
Translation factor activity,
binding
L-malate dehydrogenase activity
rRNA binding
nucleic
acid
Translation initiation factor activity
Translation factor activity, nucleic
binding
RNA binding
Actin binding
Cytoskeletal protein binding
HATCH ALL
acid
HATCH not-IEA
Biological Process
Translation
Cellular protein metabolic process
Protein metabolic process
Cellular macromolecule biosynthetic process
Translational elongation
Ribosomal small subunit biogenesis
Ribosome biogenesis
Ribonucleoprotein complex biogenesis
Cellular component biogenesis at cellular level
Regulation of cell cycle
Cellular Component
Ribosome
Ribonucleoprotein complex
Intracellular non-membrane-bounded organelle
Cytoplasm
Cytoplasmic part
Ribosome
Small ribosomal subunit
Ribosomal subunit
Cytosolic ribosome
Cytosolic small ribosomal subunit
Molecular Function
RNA binding
rRNA binding
Unfolded protein binding
Translation factor activity, nucleic
binding
Translation elongation factor activity
acid
Translation initiation factor activity
Translation factor activity, nucleic
binding
RNA binding
-
acid